Sampling array devices and system for spectral analysis

ABSTRACT

A system for use in spectral analysis procedures can include a slide and a holder for carrying the slide. The slide includes a substrate forming a plurality of wells that are recessed relative to a surface of the substrate. Each of the wells forms a sample region that is recessed by a sample depth from the surface and a trough region that is recessed by a trough depth from the surface, the trough depth being greater than the sample depth. The holder includes a body defining a cavity between a first side and a second side of the body, a port for receiving the slide into the cavity, one or more first fenestrations on the first side, and one or more second fenestrations on the second side.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.62/326,604, entitled “SAMPLING ARRAY DEVICES AND SYSTEM FOR SPECTRALANALYSIS,” filed Apr. 22, 2016, the entirety of which is incorporatedherein by reference.

BACKGROUND

Protein aggregation phenomena are prevalent throughout the industrialbioprocess. Proteins are expensive to express, isolate, and purify dueto their complex physical-chemical characteristics. Aggregation isconsidered a primary mode of protein degradation, often leading toimmunogenicity in patients, anti-drug antibody (ADA) response, and aloss of efficacy. The detection and determination of protein aggregatesis a major objective in the biopharmaceutical industry and other areasof scientific research. The formation of protein aggregates is importantin industrial applications because they can significantly affect theproduction of protein therapeutics (i.e., biologics or biosimilars),effectively lowering the production yields and increasing risk ofwithdrawal. This is at the core of analytical technologies to understandcharacterization, comparability/similarity, release and stabilitytesting of protein therapeutics. The proposed technology also lendsitself to high throughput multivariate analysis.

SUMMARY

The subject technology is illustrated, for example, according to variousaspects described as numbered clauses (1, 2, 3, etc.) for convenience.Various examples of aspects of the subject technology are describedbelow. These are provided as examples and do not limit the subjecttechnology. It is noted that any of the dependent clauses may becombined in any combination, and placed into a respective independentclause. The other clauses can be presented in a similar manner.

Clause 1. A slide comprising:

a substrate forming a plurality of wells that are recessed relative to asurface of the substrate, wherein each of the wells forms a sampleregion that is recessed by a sample depth from the surface and a troughregion that is recessed by a trough depth from the surface, the troughdepth being greater than the sample depth.

Clause 2. The slide of clause 1, wherein the substrate transmitselectromagnetic radiation.

Clause 3. The slide of clause 1, wherein the substrate is a salt.

Clause 4. The slide of clause 1, wherein the substrate comprises AgBr,AgCl, Al₂O₃, AMTIR, BaF₂, CaF₂, CdTe, CsI, diamond, Ge, KBr, KCl, KRS-5,LiF, MgF₂, NaCl, Si, SiO₂, ZnS, ZnSe, and/or ZrO₂.

Clause 5. The slide of clause 1, wherein a periphery of the slide formsa bilaterally asymmetric shape.

Clause 6. The slide of clause 1, wherein the trough region extendsentirely about the sample region.

Clause 7. The slide of clause 1, wherein the sample region isconcentrically within the trough region.

Clause 8. The slide of clause 1, wherein the plurality of wells areprovided in a plurality of rows, wherein each row comprises at least twoof the plurality of wells.

Clause 9. A system comprising

a slide comprising:

a substrate forming a plurality of wells that are recessed relative to asurface of the substrate;

a holder, comprising:

a body defining a cavity between a first side and a second side of thebody;

a port for receiving the slide into the cavity;

one or more first fenestrations on the first side; and

one or more second fenestrations on the second side.

Clause 10. The system of clause 9, further comprising a block configuredto secure the slide within the cavity when the block is placed withinthe port.

Clause 11. The system of clause 9, further comprising a cover configuredto enclose each of the wells when placed upon the surface of the slide.

Clause 12. The system of clause 11, wherein the cover is configured totransmit electromagnetic radiation.

Clause 13. The system of clause 11, wherein the cover and the slide havea substantially equal thickness in a direction orthogonal to the surfaceof the slide when the cover is placed upon the surface of the slide.

Clause 14. The system of clause 9, wherein the body of the holderabsorbs substantially all electromagnetic radiation incident to theholder.

Clause 15. The system of clause 9, wherein the plurality of wells areprovided in a plurality of rows, wherein each row comprises at least twoof the plurality of wells.

Clause 16. The system of clause 15, wherein the one or more firstfenestrations comprises a number of first windows equal to a number ofthe plurality of rows, and the one or more second fenestrationscomprises a number of second windows equal to the number of theplurality of rows.

Clause 17. The system of clause 16, wherein one of the first windows andone of the second windows are on opposite sides of one of the pluralityof rows when the slide is within the holder.

Clause 18. The system of clause 9, wherein the port is disposed on athird side of the holder.

Clause 19. The system of clause 9, wherein the first side is oppositethe second side.

Clause 20. The system of clause 9, wherein at least one of the pluralityof wells, the one or more first fenestrations, and the one or moresecond fenestrations are aligned along an axis when the slide is withinthe cavity.

Clause 21. The system of clause 9, wherein the slide, the one or morefirst fenestrations, and the one or more second fenestrations areconfigured to transmit electromagnetic radiation.

Clause 22. The system of clause 9, further comprising a coating on aninner surface of the body.

Clause 23. The system of clause 22, wherein the coating comprisessilicone.

Clause 24. The system of clause 9, further comprising a cap in thermalcontact with an outer surface of the holder, the cap comprising one ormore third fenestrations.

Clause 25. The system of clause 9, further comprising a plate attachedto an imaging device.

Clause 26. A method comprising:

providing samples to each of a plurality of wells formed in a slide,each of the wells being recessed relative to a surface of the slide;

enclosing the wells by applying a cover to the surface of the slide;

inserting the slide and the cover into a cavity of a holder; and

emitting electromagnetic radiation through one or more firstfenestrations of the holder, one or more second fenestrations of theholder, and the sample.

Clause 27. The method of clause 26, further comprising inserting theholder into a receptacle of a plate attached to an imaging device.

Clause 28. The method of clause 27, wherein inserting the holdercomprises positioning the sample at a focal length of the imagingdevice.

Clause 29. The method of clause 26, further comprising heating thesamples to a target temperature by conducting heat through the holder.

Clause 30. The method of clause 26, further comprising placing a cap inthermal contact with an outer surface of the holder.

Clause 31. The method of clause 30, wherein the emitting theelectromagnetic radiation comprises emitting the electromagneticradiation through one or more third fenestrations of the cap.

Clause 32. The method of clause 26, wherein the inserting the slide andthe cover comprises inserting the slide and the cover through a port ofthe holder.

Clause 33. The method of clause 32, further comprising, after insertingthe slide in the cover, obstructing the port with a block.

Clause 34. The method of clause 26, wherein the electromagneticradiation is infrared light.

Clause 35. The method of clause 26, further comprising, after theemitting the electromagnetic radiation, detecting a characteristic ofthe electromagnetic radiation not absorbed by the sample.

Clause 36. The method of clause 26, further comprising:

after the emitting the electromagnetic radiation, changing thetemperature of the sample; and

emitting additional electromagnetic radiation through the one or morefirst fenestrations and the one or more second fenestrations of theholder and through the sample.

Additional features and advantages of the subject technology will be setforth in the description below, and in part will be apparent from thedescription, or may be learned by practice of the subject technology.The advantages of the subject technology will be realized and attainedby the structure particularly pointed out in the written description andclaims hereof as well as the appended drawings.

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory and areintended to provide further explanation of the subject technology asclaimed.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are included to provide furtherunderstanding of the subject technology and are incorporated in andconstitute a part of this description, illustrate aspects of the subjecttechnology and, together with the specification, serve to explainprinciples of the subject technology.

FIG. 1A shows a perspective view of a slide in accordance with someembodiments of the subject technology.

FIG. 1B shows a top view of the slide of FIG. 1A in accordance with someembodiments of the subject technology.

FIG. 1C shows a side view of the slide of FIG. 1A in accordance withsome embodiments of the subject technology.

FIG. 1D shows a bottom view of the slide of FIG. 1A in accordance withsome embodiments of the subject technology.

FIG. 1E shows a sectional view of a portion of the slide of FIG. 1A,including a well, in accordance with some embodiments of the subjecttechnology.

FIG. 2A shows a perspective view of a cover and the slide of FIG. 1A inaccordance with some embodiments of the subject technology.

FIG. 2B shows a perspective view of the cover of FIG. 2A and the slideof FIG. 1A in accordance with some embodiments of the subjecttechnology.

FIG. 3A shows a perspective view of a cap in accordance with someembodiments of the subject technology.

FIG. 3B shows a top view of the cap of FIG. 3A in accordance with someembodiments of the subject technology.

FIG. 3C shows a side view of the cap of FIG. 3A in accordance with someembodiments of the subject technology.

FIG. 3D shows a front side view of the cap of FIG. 3A in accordance withsome embodiments of the subject technology.

FIG. 4A shows a perspective view of a holder in accordance with someembodiments of the subject technology.

FIG. 4B shows another perspective view of the holder of FIG. 4A inaccordance with some embodiments of the subject technology.

FIG. 4C shows a top view of the holder of FIG. 4A in accordance withsome embodiments of the subject technology.

FIG. 4D shows a front view of the holder of FIG. 4A in accordance withsome embodiments of the subject technology.

FIG. 4E shows a side view of the holder of FIG. 4A in accordance withsome embodiments of the subject technology.

FIG. 5A shows a perspective view of a block in accordance with someembodiments of the subject technology.

FIG. 5B shows a side view of the block of FIG. 5A in accordance withsome embodiments of the subject technology.

FIG. 5C shows a front view of the block of FIG. 5A in accordance withsome embodiments of the subject technology.

FIG. 5D shows a top view of the block of FIG. 5A in accordance with someembodiments of the subject technology.

FIG. 6A shows a perspective view of the slide of FIG. 1A, the cover ofFIG. 2A, the cap of FIG. 3A, and the holder of FIG. 4A in accordancewith some embodiments of the subject technology.

FIG. 6B shows a perspective view of the holder of FIG. 4A and the blockof FIG. 5A in accordance with some embodiments of the subjecttechnology.

FIG. 6C shows a sectional view of portions of the slide of FIG. 1A, thecover of FIG. 2A, the cap of FIG. 3A, and the holder of FIG. 4A inaccordance with some embodiments of the subject technology.

FIG. 7 shows a perspective view of a slide in accordance with someembodiments of the subject technology.

FIG. 8 shows a perspective view of a cap in accordance with someembodiments of the subject technology.

FIG. 9 shows a perspective view of a holder in accordance with someembodiments of the subject technology.

FIG. 10A shows a top view of a plate in accordance with some embodimentsof the subject technology.

FIG. 10B shows a top view of the holder of FIG. 4A and the plate of FIG.7A in accordance with some embodiments of the subject technology.

FIG. 11 shows a schematic view of the holder of FIG. 4A and the plate ofFIG. 7A in accordance with some embodiments of the subject technology.

DETAILED DESCRIPTION

In the following detailed description, specific details are set forth toprovide an understanding of the subject technology. It will be apparent,however, to one ordinarily skilled in the art that the subjecttechnology may be practiced without some of these specific details. Inother instances, well-known structures and techniques have not beenshown in detail so as not to obscure the subject technology.

The biologics and biosimilar industry is involved in the research,development, and manufacturing of complex drugs known as proteintherapeutics. The research and development efficiency can be undesirablylow, which increases costs of drug development due to the high attritionrate of protein therapeutics. The costs of protein therapeuticdevelopment is significantly impacted by early and late stage failure.One way to lower research and development costs is to perform a seriesof evaluations of the protein therapeutic candidate early in theresearch and development phase. By performing the characterization ofthe therapeutic protein under varying formulation conditions andstressors early in the research and development phase, a predictiveprofile of the therapeutic candidate is generated to assess the risk ofprotein aggregation. This approach has been defined as a developabilityassessment. This assessment can provide important information fordecision making, such as selecting protein therapeutic candidates forfurther development. When protein aggregation occurs the proteintherapeutic typically has decreased efficacy and can elicit an immuneresponse. In severe cases, such an immune response can be fatal.

The problem of protein aggregation is complex and frequently involvesseveral different chemical processes, which are difficult to discern.Aggregation may be stress induced and involve physical or chemicalchanges such as agitation or stirring, oxidation, deamination andtemperature changes. Even a slight change in pH, salt conditions,protein concentration or formulation conditions can also induce proteinaggregation. Again, aggregation leads to lower yields in production,loss of efficacy of the protein therapeutic, and safety concerns inrelation to immunogenicity risks. Currently, available techniques toassess aggregation do not address all of the factors that are involvedin the process, such as the size, identity, mechanism and extent ofaggregation, and stability of the protein therapeutic in solution.Several techniques have been developed to address the size of theaggregate or particulate, yet they do not determine the identity. Othertechniques can determine the size and the identity of aggregates, butcannot determine the extent of aggregation or identify the aggregationprone regions. The amino acid side chains present in a protein areimportant contributors to the stability of proteins. Yet to date, withthe available routine high throughput bench instrumentation therelationship between the weak chemical interactions involving sidechains and the stability of the secondary structure of the proteincandidate has not been ascertained.

The stability of the protein therapeutic is also critical for drugdevelopment, and cannot be fully characterized by simply identifying thethermal transition temperature of the protein. A greater level ofunderstanding is needed to fully address the stability of proteintherapeutics. For example it would be beneficial to understand 1) therelative stability of the domains within the protein of interest, 2) howthe amino acid side chains contribute to the stability the domains, 3)whether the amino acid side chains are involved in the aggregationmechanism, and 4) if an excipient can stabilize weak interactions (e.g.,in amino acid side chains) within the critical regions in specificdomains of the protein therapeutic. There is a gap in understanding thefactors that are important for determining the mechanism of proteinaggregation.

To date when commercially available techniques are used orthogonally,differences in the sensitivity of the available techniques is a concern.In general, such techniques focus on determining the size, purity andstability of the protein therapeutic, and evaluate the presence orabsence of protein aggregates or particulates in a formulation, toachieve lot-to-lot consistency.

There is a need for technology that can be used to better assess thedevelopability of protein therapeutics, and for the comparabilityassessments needed to maintain and ensure product integrity, efficacyand safety. Such a process would need to be recognized as sufficient toensure product integrity, efficacy and safety by the Food and DrugAdministration (FDA) Center for Drug Evaluation (CDER) division andother relevant regulatory bodies.

Aspects of the subject technology provide a fast, accurate, andreproducible technique to determine the size, identity, mechanism, andextent of aggregation and the stability of a protein therapeutic, orother chemicals, in a single experiment. Aspects of the subjecttechnology address comparability assessment of different proteintherapeutic candidates and developability assessment of proteintherapeutic candidates.

Aspects of the subject technology provide a system that includesreusable components, requires small sample sizes, reduces or eliminatessample evaporation, provides excellent signal/noise ratio with noobserved fringes, a fixed path length relative to an imaging deviceallowing for quantitative analysis, excellent comparability assessmentassays, developability assessment using Design of Experiment (DOE)approach, and assessment of aggregation reversibility during a thermaldependence study.

Aspects of the subject technology provide a sample carrying device withenhanced thermal conductivity, ease of loading and unloading, enhancedsecurement of samples, uniform temperature distribution, optimalfocusing with an imaging device, and high throughput data acquisition.

According to some embodiments, for example as shown in FIGS. 1A-IE, aslide 100 can include a substrate 110 that forms a plurality of wells150. Each of the wells 150 can be recessed relative to a surface 130 ofthe substrate 110. The surface 130 can be substantially flat or planarexcept where a well 150 is present. As used herein, a substantially flator planar surface is one that varies from exactly flat or planar withina tolerance that is typical for an applicable manufacturing process.Each of the wells 150 can form a sample region 160 for receiving asample to be analyzed and a trough region 170 for receiving excessportions of the sample.

The wells 150 can be provided in separate rows 140. For example, a firstrow 140 can include a first number of wells 150, and a second row 140can include a second number of wells 150. The rows 140 can include thesame number of wells 150 or different numbers of wells 150. The slide100 can include any number of rows 140 and any number of wells 150within each row 140. For example, the slide 100 can include one, two,three, four, five, six, seven, eight, nine, or more than nine rows 140.Each row 140 can include one, two, three, four, five, six, seven, eight,nine, or more than nine wells 150. The number of rows 140 and wells 150can be selected based on a desired number of separate samples to besimultaneously analyzed on a single slide 100.

According to some embodiments, the slide 100 can be used to analyze alarge number of samples along with a reference in the same slide 100.One of the wells 150 can be provided with the reference for analysisunder the same conditions (e.g., temperature, humidity, etc.) as thoseof the samples on the slide 100. According to some embodiments, featuresof the slide 100 can provide an indication regarding the identity ofparticular wells 150. For example, as shown in FIGS. 1A-ID, a shape ofthe slide 100 can include a number of corners. Some of the corners canbe regular corners 120 that have common features (e.g., right angle atintersecting surfaces). One or more of the corners can be an irregularcorner 122 that has at least one feature that is different from thecommon feature of the regular corners 120. The resulting shape (e.g.,perimeter) of the slide 100 can be asymmetric. For example, the shape ofthe slide 100 can be bilaterally asymmetric across one or more axes. Asshown in FIG. 1D, at least a portion of the irregular corner 122 canform an angle 124 that is different (e.g., 45 degrees) from the angleformed at the regular corners 120. The location of the irregular corner122 can be used for identifying and distinguishing the separate wells150. For example, a reference can be provided within the well 150 thatis closest to the irregular corner 122. By further example, samples canbe provided to the wells 150 other than the well 150 that is closest tothe irregular corner 122. At various stages before, during, and afteranalysis, the well 150 containing the reference can be identified basedon the location of the irregular corner 122.

According to some embodiments, the slide 100 can include a substrate110. Preferably, the substrate can transmit electromagnetic radiation,such as visible and/or infrared light, and is suitable for use inspectral analysis. The substrate 110 can be entirely of a singlesubstrate material or a composite of multiple materials. The material ofthe substrate 110 can be selected for facilitating spectral analysis ofa reference or sample received within wells 150 of the slide 100. Forexample, the material of the substrate 110 can transmit visible and/orinfrared light and be substantially non-reactive with the referenceand/or the sample. The substrate 110 can include a salt. The substrate110 can include AgBr, AgCl, Al₂O₃, amorphous material transmittinginfrared radiation (“AMTIR”), BaF₂, CaF₂, CdTe, water clear zinc sulfide(e.g., Cleartran™), CsI, diamond, Ge, KBr, KCl, red thallium bromoiodide(“KRS-5”), LiF, MgF₂, NaCl, Si, SiO₂, ZnS, ZnSe, ZrO₂, and/orcombinations thereof. The substrate 110 can be coated or uncoated.Slides 100 of the type described herein can be reused multiple times inseparate procedures with different references and samples.

According to some embodiments, for example as shown in FIGS. 1B and 1E,each of the wells 150 can form a sample region 160 that is recessed by asample depth 162 from the surface 130. Each of the wells 150 can alsoform a trough region 170 that is recessed by a trough depth 172 from thesurface 130. The trough region 170 can extend entirely about the sampleregion 160. For example, the sample region 160 can be concentricallywithin the trough region 170 with respect to an axis extendingorthogonally to the surface 130. The sample region 160 and the troughregion 170 can be formed by removing portions on the surface 130 of thesubstrate 110. For example, a milling process or other process forremoving material can be applied to the surface 130 to form the sampleregion 160 and the trough region 170. The sample region 160 of thetrough region 170 can be formed in the same or separate processes.

The sample region 160 can span an outer sample cross-sectional dimension164 in at least one direction. A volume of a reference or sample thatcan be received within the sample region 160 can be defined, at least inpart, by the sample depth 162 and the outer sample cross-sectionaldimension 164. At least a portion of the sample region 160 can bepositioned within a field of view of an imaging device 800 or otherequipment.

The trough region 170 can span a trough cross-sectional dimension 174 inat least one direction. The trough cross-sectional dimension 174 can bedefined by the difference between an outer trough cross-sectionaldimension 154 and the outer sample cross-sectional dimension 164. Avolume of a reference or sample that can be received within the troughregion 170 can be defined, at least in part, by the trough depth 172 andthe trough cross-sectional dimension 174. The trough depth 172 can begreater than the sample depth 162. For example, the trough depth 172 canbe more than double, more than five times, or more than ten times thesample depth 162.

The outer sample cross-sectional dimension 164 can be about 2.0 mm. Thesample depth 162 can be about 0.04-0.08 mm±0.01 mm ideal for D₂Ocontaining samples or 0.004-0.012 mm±0.002 mm H₂O containing samples.For example, the sample depth 162 can be about 0.04 mm or about 0.07 mm.A greater sample depth 162 can facilitate a greater concentration rangeof proteins for analysis. The trough cross-sectional dimension 174 canbe about 1.0 mm. The outer trough cross-sectional dimension 154 can beabout 6.0 mm. The trough depth 172 can be about 0.60 mm. Spacing betweencenters of adjacent wells 150 can be greater than the outer troughcross-sectional dimension 154. These exemplary dimensions can bemodified as needed to suit a given purpose.

According to some embodiments, the trough region 170 can receive anamount of a reference or sample that exceeds the volume of the sampleregion 160. For example, as a sample or references applied to the sampleregion 160, and the amount that does not fit within the sample depth 162and the outer sample cross-sectional dimension 164 can move to thetrough region 170. Such action may occur during application of thereference or sample or during application of a cover 200 to the slide100. The trough region 170 can be of adequate volume to accommodate allexcessive amounts of the reference or sample. The trough region 170 canbe wide and deep enough to prevent portions of the reference or samplefrom overflowing out of both the sample region 160 and the trough region170 (i.e., onto the surface 130). As such, an entire amount of thereference or sample can be contained entirely within the well 150 andprevent cross contamination with the contents of any other well 150.

According to some embodiments, for example as shown in FIGS. 2A-2B, acover 200 can be applied to the slide 100. An opposing surface 230 ofthe cover 200 can be substantially flat or planar. Some features of thecover 200 can be complementary or identical to features of the slide100. For example, a shape of the cover 200 can include a number ofcorners. Some of the corners of the cover 200 can be regular corners 220that are identical or similar to the regular corners 120 of the slide100. One or more of the corners of the cover 200 can be an irregularcorner 222 that are identical or similar to the irregular corner 122 ofthe slide 100. The resulting shape (e.g., perimeter) of the cover 200can be identical or similar to the shape (e.g., perimeter) of the slide100.

According to some embodiments, the cover 200 can include a substrate210. Preferably, the substrate can transmit electromagnetic radiation,such as visible or infrared light, and is suitable for use in spectralanalysis. The substrate 210 can be of the same material as or adifferent material from that or the substrate 110 of the slide 100. Thematerial of the substrate 210 can be selected for facilitating spectralanalysis of a reference or sample received within wells 150 of the slide100. For example, the material of the substrate 210 can transmit visibleand/or infrared light and be substantially non-reactive with thereference and/or the sample. Covers 200 of the type described herein canbe reused multiple times in separate procedures with differentreferences and samples.

The opposing surface 230 of the cover 200 can be brought into contactwith the surface 130 of the slide 100. In such a configuration, theopposing surface 230 can be parallel to or coplanar with the surface130. When the cover 200 is brought into contact with the slide 100, theopposing surface 230 can extend over one or more of the wells 150 of theslide 100. The opposing surface 230 can enclose each of the wells 150,such that each well 150 is isolated from an external environment andfrom every other well 150. The cover 200 can prevent evaporation of thereference or sample from the well 150. The boundary of each of thesample region 160 and the trough region 170 can be defined, in part, bythe opposing surface 230. Application of the cover 200 to the slide 100can cause at least a portion of a reference or sample within the sampleregion 160 to move into the trough region 170.

The cover 200 can define a cover thickness 212 in a dimension that isorthogonal to the opposing surface 230. Additionally, the slide 100 candefine a slide thickness 112 and a dimension that is orthogonal to thesurface 130. The cover thickness 212 can be equal to or substantiallyequal to the slide thickness 112. As used herein, a substantially equalthickness is one that varies from exactly equal within a tolerance thatis typical for an applicable manufacturing process.

According to some embodiments, for example as shown in FIGS. 3A-3D, acap 300 can be provided for conduction of heat across portions of theslide 100 and/or the cover 200. The cap 300 can include a cap surface330 that is substantially flat or planar. One or more support rails 360can protrude from the cap surface 330. One or more cap fenestrations 350can extend through a portion of the cap 300, including the cap surface330. The one or more cap fenestrations 350 can form windows that areeach configured to be aligned with a corresponding one of the rows 140of the slide 100. The number of cap fenestrations 350 can be equal tothe number of rows 140 of the slide 100. Each of the cap fenestrations350 can span a length that encompasses all of the wells 150 of thecorresponding row 140. The one or more cap fenestrations 350 providetransmission of electromagnetic radiation to and/or from the wells 150of the slide 100. Heat can be transmitted between the cap 300 andadjacent components. At least a portion of the cap 300 can be of amaterial with high thermal conductivity. Exemplary materials for thebody 410 include aluminum, polytetrafluoroethylene (“PTFE”), brass,bronze, copper, silver, gold, and other metal alloys or ceramic.

According to some embodiments, for example as shown in FIGS. 4A-4E, aholder 400 can contain and support the slide 100 and/or the cover 200. Abody 410 of the holder 400 can define a cavity 420 between a first side412 and a second side 414 of the body 410. A port 470 provides access tothe cavity 420 for receiving the slide 100 and/or the cover 200 into thecavity 420.

According to some embodiments, one or more first fenestrations 450 canextend through a portion of the first side 412 of the body 410. One ormore second fenestrations 460 can extend through a portion of the secondside 414 of the body 410. The first fenestrations 450 and/or the secondfenestrations 460 can form windows that are each configured to bealigned with a corresponding one of the rows 140 of the slide 100 whenthe slide 100 is placed in the holder 400. The number of firstfenestrations 450 and/or the number of second fenestrations 460 can beequal to the number of rows 140 of the slide 100. Each of the firstfenestrations 450 and/or the second fenestrations 460 can span a lengththat encompasses all of the wells 150 of the corresponding row 140. Thefirst fenestrations 450 and/or the second fenestrations 460 providetransmission of electromagnetic radiation to and/or from the wells 150of the slide 100.

According to some embodiments, the cavity 420 of the holder 400 is sizedsuch that an inner surface 422 of the holder contacts at least a portionof the slide 100 and/or the cover 200. The inner surface 422 can providethermal contact with at least one of the slide 100 and/or the cover 200.For example, the inner surface 422 on the first side 412 can contact thecover 200 and the inner surface 422 on the second side 414 can contactthe slide 100. Heat can be transmitted between the holder 400 and itscontents. At least a portion of the body 410 of the holder 400 can be ofa material with high thermal conductivity, sturdy construction, andlow-electromagnetic radiation (e.g, visible light, infrared light,quantum cascade laser) reflection. Exemplary materials for the body 410include anodized aluminum, PTFE, bronze, and copper. The holder 400 canabsorb a substantial amount of electromagnetic radiation that isincident thereon. For example, the holder 400 can absorb at least 90%,at least 95%, or at least 99% of the electromagnetic radiation that isincident thereon. As the holder 400 absorbs more electromagneticradiation than it reflects, the holder 400 reduces interference withaccurate readings during a spectral analysis. At least a portion of theinner surface 422 can be provided with a coating to reduce or eliminatedamage to the contents of the holder 400 when moving or residingtherein. Exemplary materials for the coating include silicone.

According to some embodiments, one or more extensions 430 can beprovided at an outer periphery of the holder 400. The extensions 430 canprovide guidance and slideable engagement with a portion of otherequipment for aligning the reference and samples within a field view ofan imaging device 800.

According to some embodiments, the port 470 can be provided on any sideof the holder 400. For example, the port 470 can be provided on a sideof the holder 400 that has a length shorter than at least one other sideof the holder 400. Alternatively or in combination, the port 470 can beprovided on a side of the holder 400 that has a length longer than atleast one other side of the holder 400. The port 470 can be adjacent toa receptacle 480 for receiving a block 500. The receptacle 480 caninclude a groove, recess, channel, rail, or other guide for receivingthe 502 partially or entirely obstructing the port 470.

According to some embodiments, for example as shown in FIGS. 5A-5D, ablock 500 can be used to secure items within the cavity 420 of theholder 400. The block 500 may include a barrier 520 configured to fitwithin the receptacle 480 of the holder 400. The barrier 520 can befurther configured to partially or entirely obstruct the port 470, suchthat contents within the cavity 420 of the holder 400 remain within thecavity 420 until the block 500 is removed. For example, the slide 100and/or the cover 200 can be secured within the cavity 420 while theblock 500 is within the receptacle 480. The block 500 can also include ahandle 530 for use during operation by a user.

According to some embodiments, for example as shown in FIGS. 6A-6B, anassembly can be formed of the components described herein. One or morereferences and samples are provided to each of a plurality of wells 150formed in the slide 100. The wells 150 are enclosed by applying thecover 200 to of the slide 100. For example, the opposing surface 230 ofthe cover 200 can be applied to the surface 130 of the slide 100. Theslide 100 and/or the cover 200 can be inserted through the port 470 andinto the cavity 420 of the holder 400. According to some embodiments,the cap 300 can be applied to the holder 400. For example, the Surface330 can be applied to a side of the holder 400, such as the first side412. In such a configuration, the cap fenestrations 350 can be alignedwith the first fenestrations 450. At least one of the support rails 360of the cap 300 can contact and/or rest on one or more of the extensions430 of the holder 400. The cap 300 can be in thermal contact with one ormore sides of the holder 400 to facilitate heat distribution across theholder 400. The cap 300 can provide thermal control through intimatecontact with an etched foil that is equipped with resistance temperaturedetectors, thermocouples, and/or other sensors. Features (e.g.,thermocouples and/or sensors) of the cap 300 can be connected to one ormore control components, such as a PLC controller. By heating in ahomogeneous fashion, the cap 300 allows a continuous and gradient-freeheat transfer along a region of contact with the holder 400. The cap 300can shield the holder 400 from a cool draft of a microscope purge. Oneor more of the features of the cap 300, as described herein, can beprovided exclusively on the cap 300 and not on the holder 400, such thatthe one or more features can be omitted when the holder 400 is usedwithout the cap 300. Additionally, features of the cap 300 connecting toother components of the system (e.g., PLC controller, etc.) can remainconnected to a cap 300 while various holders 400 can each be used inconjunction with the cap 300 without requiring connection anddisconnection of the features. According to some embodiments, with thecontents (not shown in FIG. 6B) within the cavity 420 of the holder 400,the block 500 can be inserted into the receptacle 480 of the holder 400to secure the contents within the cavity 420.

The cap 300 can include an etched foil heater that controls thetemperature of samples in the slide. The etched foil heater spans asurface of the cap 300. A foil layer of the heater can be between one orboth of a base laminate layer and a cover laminate layer. The laminatelayers can include a dielectric material (e.g., polyimide) forelectrically isolating the etched foil from the cap 300 and/or otherstructures. The etched foil can have a pair of terminals with leads on aside of the cap 300 that allow a user to connect a power supply (e.g.,DC power) to the etched foil heater. Between the terminals, the etchedfoil heater can define a pathway that traverses the cap 300. Forexample, the pathway can extend about and between each and every one ofthe cap fenestrations 350. The etched foil heater can distribute heatevenly across the cap 300 and thereby transfer heat evenly to the slide,so that temperature gradients across the cap 300 and the slide arereduced or eliminated. The etched foil heater can have a temperaturethreshold, above which the heater activity will cease automatically.According to some embodiments, a base (not shown) similar to the cap 300can be provided for application to the cover 200. The base can beprovided on a side of the cover opposite the cap 300. The base can be amirror image of the cap 300 and have features that are identical to thatof cap 300. For example, the base can include fenestrations that alignwith the second fenestration 460. By further example, the base caninclude an etched foil heater.

According to some embodiments, for example as shown in FIG. 6C, thecomponents described herein can be stacked to align a reference orsample with an imaging axis 1000. Along the imaging axis 1000, the capfenestration 350, the first fenestration 450, the cover 200, the slide100 (including the sample region 160), and/or the second fenestration460 can be aligned. Electromagnetic radiation can be transmitted througheach of the above components in either or both directions along theimaging axis 1000.

According to some embodiments, for example as shown in FIGS. 7-9, anynumber of samples can be evaluated by providing an appropriate number ofwells in a slide and corresponding structures to accommodate the wells.For example, as shown in FIG. 7, the slide 100 can include a substratethat forms a plurality of wells 150 provided in separate rows 140. Asshown in FIG. 7, three rows 140 can be provided. For example, a firstrow 140 can include a first number of wells 150, a second row 140 caninclude a second number of wells 150, and a third row 140 can include athird number of wells 150. The rows 140 can include the same number ofwells 150 or different numbers of wells 150. According to someembodiments, the cap 300 can include a number of cap fenestrations 350that corresponds to the number of rows 140 of the slide 100. Forexample, three cap fenestrations 350 can form windows that areconfigured to be aligned with the three rows 140 of the slide 100.According to some embodiments, the holder 400 can include a number offirst fenestrations 450 and second fenestrations 460 that thatcorrespond to the number of rows 140 of the slide 100. For example,three first fenestrations 450 and three second fenestrations 460 canform windows that are configured to be aligned with the three rows 140of the slide 100.

According to some embodiments, for example as shown in FIGS. 10A-11, aplate 700 can receive the holder 400, its contents, and/or the cap 300.The plate 700 can be a component of an imaging device 800 or beconfigured to attach to an imaging device 800 during operation thereof.The imaging device 800 can include a microscope, a camera, a mirror, alens, quantum cascade lasers, or an infrared source with a beamsplitter, a detector, a sensor, or combinations thereof. The imagingdevice 800 can be configured to capture information regardingelectromagnetic radiation incident upon the reference or sample withinthe sample region 160. The plate 700 can include a body 710 and a window750 that transmits electromagnetic radiation to or from the slide 100.At the location of the window 750, the plate 700 can provide a recessedregion for receiving the holder 400.

According to some embodiments, the plate 700 can facilitate alignment tobring the sample region 160 within a field of view and a focal lengthand/or focal plane of the imaging device 800. For example, the plate 700can include one or more guide 740 for receiving the holder 400. At leasta portion of the holder 400, such as the extensions 430, can be receivedwithin the guides 740. The holder 400 can move along a positioning axis790. The positioning axis 790 can be parallel to one or more of the rows140 of the slide 100. As the holder 400 is moved along the positioningaxis 790, a selected one or more of the sampling regions 160 can bealigned to be within a field of view of the imaging device 800. Theholder 400 can move along the positioning axis 790 manually or by anautomated or programmed mechanism 810, such as a servo-motor and/orstepper motor. The mechanism 810 can be controlled by a controller, suchas the controller connected to the cap 300. For a variety of positionsof the holder 400 within the plate 700, the sample region 160 that iswithin a field of view of the imaging device 800 will be a fixed andconsistent distance (e.g., focal distance) from a reference point (e.g.,electromagnetic radiation source). Accordingly, a fixed path length foran electromagnetic radiation beam can be determined and maintainedthroughout a procedure in which multiple references and/or samples areanalyzed.

According to some embodiments, the path length for an electromagneticradiation beam can vary for multiples samples in multiple wells of aslide. The path length can vary to ensure that sample concentration isthe same or similar for different samples. The path length can bedetermined based on the Beer-Lambert law (or Beer's law), whichdemonstrates the linear relationship between absorbance andconcentration of an absorbing species. The general Beer-Lambert law isusually written as:

A=ε(λ)*b*c,

where A is the measured absorbance, ε(λ) is a wavelength-dependentabsorptivity coefficient, b is the path length, and c is the analyteconcentration. When working in concentration units of molarity, theBeer-Lambert law is written as:

A=ε*b*c,

where ε is the wavelength-dependent molar absorptivity coefficient withunits of M⁻¹ cm⁻¹. Experimental measurements can be made in terms oftransmittance (T), which is defined as:

T=I/I ₀

where I is the light intensity after it passes through the sample and I₀is the initial light intensity. The relation between A and T is:

A=−log T=−log(I/I ₀).

Modern absorption instruments can usually display the data as eithertransmittance, %-transmittance, or absorbance. An unknown concentrationof an analyte can be determined by measuring the amount of light that asample absorbs and applying Beer's law. If the absorptivity coefficientis not known, the unknown concentration can be determined using aworking curve of absorbance versus concentration derived from standards.

Calibration of path lengths (i.e., well depths) for wells of a slide canbe performed, for example, by analyzing absorbance results. Where themeasurements of absorbance can be linearly correlated with the knownpath lengths and where deviations from this correlation are observed,corrections to the path lengths can be made to account for the lack oflinearity. The variable path lengths can then compensate for thedeviations from the linear correlation, so that further tests during acalibration stage provide results that are consistent with the linearcorrelation.

The plate 700, for example as shown in FIG. 10B, can include features(e.g., recesses 760) to accommodate other components of the samplingsystem 1, for example as shown in FIG. 11, such as heating elements 830,cooling elements 840 (e.g., Peltier, embedded microfluidic/TEG system),and/or temperature sensors 850 (e.g., thermocouples) to uniformly heatand monitor temperature conditions of the plate 700. The plate 700 canalso be provided with humidity sensors 860 for determining a humiditylevel in a sampling compartment of the imaging device 800. Alternativelyor in combination, the cap 300 and/or the holder 400 can includefeatures (e.g., recesses 390) to include heating elements, coolingelements (e.g., Peltier), temperature sensors (e.g., thermocouples),and/or connection ports connecting to one or more of the above touniformly heat and monitor temperature conditions of the holder 400and/or its contents. Output of one or more sensors of the system canprovide data to a controller 820, such as a Peripheral InterfaceController (“PIC”) microcontroller. Temperature conditions can beregulated by the controller 820 based on data from sensors. Thecontroller 820 can further control operation of any heat elements arecooling elements to provide uniform temperature conditions across theslide 100. Heat can be transmitted across the plate 700, the holder 400,and/or its contents. At least a portion of the body 710 of the plate 700can be of a material with high thermal conductivity, sturdyconstruction, and low electromagnetic radiation reflection. Exemplarymaterials for the body 710 include anodized aluminum, PTFE, bronze, andcopper.

The controller 820 can raise or lower temperatures in multiple (e.g., 3or more) positions according to a user defined instructions and/orinputs. Once a target temperature has been reached, the assembly (e.g.,holder 400) can move to a first measuring position. Multiple (e.g., 3 ormore) measuring positions can be achieved to capture information withrespect to all wells in the assembly. At a given target temperature, ameasuring cycle can include of the following steps: (1) reach correcttemperature in all heaters; (2) send a “ready to measure” signal to themicroscope; (3) wait until the microscope returns an “end ofmeasurement” signal; (4) move the assembly to the next position.Relative humidity and temperature for each well can be measured andrecorded. The system can control a servo or stepper motor to move theassembly through appropriate well alignments. Each position can bemaintained for a time specified as part of the experiment parameters.The limits of assembly movement can be indicated by end limit switches.The controller 820 can sense and be provided with an indication when thetarget well is in position for measurement. The controller 820 canprovide a user interface for a user to enter and modify one or moretarget temperatures and/or other parameters for an experiment. A fullcycle can include ascending temperatures and/or descending temperatures.The controller 820 can include a feature that provides an indication(e.g., alarm) to a user based on occurrence of particular conditions,such as failure to maintain temperature during measurements and/orfailure to maintain relative humidity within a range.

According to some embodiments, multiple (e.g., four) different zoneswill define the sampling array of the sampling system 1 which will befully automated with the servo-motor to allow for the advancement of theholder 400 through the field of view of the imaging device 800. Thecontrol of the servo-motor to predefined positions and the cyclingthereof can be facilitated by a controller 820. Thus, data acquisitioncan be fully automated along with temperature control of the holder 400and its contents.

According to some embodiments, multiple data acquisition stages can beperformed in which a plurality of references and/or samples areevaluated under a first set of conditions (e.g., temperature, humidity,etc.), followed by a change in the conditions and further evaluation ofat least some of the same references and/or samples under the newconditions.

According to some embodiments, additional data acquisition stages can beperformed in which the plurality of references and/or samples arereturned to the first set of conditions (e.g., temperature, humidity,etc.), followed by further evaluation to assess reversibility under oneor more condition dependencies (e.g., thermal dependency).

According to some embodiments, the sampling system 1 described hereincan be used for determining the mechanism of aggregation and the amountof aggregation in protein, peptide or peptoid formulation, in solutionor lyophilized state without the use of probes or additives byperforming a Fourier transform infrared (“FT-IR”) and two-dimensionalcorrelation analysis (“2DCOS”) analysis, for example as described inU.S. Pat. No. 8,268,628, hereby incorporated herein by reference. Suchanalysis can be performed by a computing system 890. FT-IR spectroscopyallows for a high degree of flexibility and speed in the determinationof protein aggregates, with limited manipulation and without the use ofexogenous probes. A sample and/or reference of the sampling system 1 isheated and left to equilibrate followed by spectral acquisition at thedesired temperature and the determination of protein, peptide andpeptoid, stability, aggregation and viability can be performed. Themethod can also be applied to the study of lipids, membrane proteins,hydrophilic proteins, peptides and peptoids as a single component or inbinary or ternary mixtures with other peptides, or lipid mixtures.

When studying two protein components in a mixture or complex, one of thecomponents can be isotopically labeled to allow for the simultaneousdetection of each component. FT-IR spectroscopy can be combined with the2DCOS which allows for determination of the presence of aggregates anddetermination of the mechanism of aggregation. This information can thenbe used to alter the protein manufacturing process to generate a moreviable protein for development. In addition, the thermal transition ofthe protein can also be determined and a 2DCOS plot generated to comparewith the established viable protein, allowing for quality control,stability, and viability of the desired protein product.

According to some embodiments, the sampling system 1 is not limited toanalyzing proteins, peptides or peptoids, but may be used to analyze anydesired composition such as a liquid sample, lipid, or polymers duringthermal or other perturbation. According to one aspect of the subjecttechnology, the dual cell holder can be applied to the study ofsubstances (organic or inorganic), materials or reagents, and liquids ingeneral. According to some embodiments, the dual cell holder can be usedin spectrophotometers where a shuttle or automated method of sampling isused. According to some embodiments, the use of the sampling system 1 isnot limited to the infrared range, but can also be used in UV andvisible range, as well as circular dichroism (CD), vibrational circulardichroism, and Raman spectroscopies, for example, for the analysis ofdesired materials and substances.

According to some embodiments, the sampling system 1 can be used todetermine protein-protein interactions (“PPI's”) orprotein-macromolecules (protein-lipid interactions, protein DNA orprotein-RNA interactions or protein drug interactions). Also, thesampling system 1 can be used for the analysis of organic solutions,polymers, gels, nanostructures or small liquid crystals, etc.

A phrase such as “an aspect” does not imply that such aspect isessential to the subject technology or that such aspect applies to allconfigurations of the subject technology. A disclosure relating to anaspect may apply to all configurations, or one or more configurations.An aspect may provide one or more examples of the disclosure. A phrasesuch as “an aspect” may refer to one or more aspects and vice versa. Aphrase such as “an embodiment” does not imply that such embodiment isessential to the subject technology or that such embodiment applies toall configurations of the subject technology. A disclosure relating toan embodiment may apply to all embodiments, or one or more embodiments.An embodiment may provide one or more examples of the disclosure. Aphrase such “an embodiment” may refer to one or more embodiments andvice versa. A phrase such as “a configuration” does not imply that suchconfiguration is essential to the subject technology or that suchconfiguration applies to all configurations of the subject technology. Adisclosure relating to a configuration may apply to all configurations,or one or more configurations. A configuration may provide one or moreexamples of the disclosure. A phrase such as “a configuration” may referto one or more configurations and vice versa.

The foregoing description is provided to enable a person skilled in theart to practice the various configurations described herein. While thesubject technology has been particularly described with reference to thevarious figures and configurations, it should be understood that theseare for illustration purposes only and should not be taken as limitingthe scope of the subject technology.

There may be many other ways to implement the subject technology.Various functions and elements described herein may be partitioneddifferently from those shown without departing from the scope of thesubject technology. Various modifications to these configurations willbe readily apparent to those skilled in the art, and generic principlesdefined herein may be applied to other configurations. Thus, manychanges and modifications may be made to the subject technology, by onehaving ordinary skill in the art, without departing from the scope ofthe subject technology.

It is understood that the specific order or hierarchy of steps in theprocesses disclosed is an illustration of exemplary approaches. Basedupon design preferences, it is understood that the specific order orhierarchy of steps in the processes may be rearranged. Some of the stepsmay be performed simultaneously. The accompanying method claims presentelements of the various steps in a sample order, and are not meant to belimited to the specific order or hierarchy presented.

As used herein, the phrase “at least one of” preceding a series ofitems, with the term “and” or “or” to separate any of the items,modifies the list as a whole, rather than each member of the list (i.e.,each item). The phrase “at least one of” does not require selection ofat least one of each item listed; rather, the phrase allows a meaningthat includes at least one of any one of the items, and/or at least oneof any combination of the items, and/or at least one of each of theitems. By way of example, the phrases “at least one of A, B, and C” or“at least one of A, B, or C” each refer to only A, only B, or only C;any combination of A, B, and C; and/or at least one of each of A, B, andC.

Terms such as “top,” “bottom,” “front,” “rear” and the like as used inthis disclosure should be understood as referring to an arbitrary frameof reference, rather than to the ordinary gravitational frame ofreference. Thus, a top surface, a bottom surface, a front surface, and arear surface may extend upwardly, downwardly, diagonally, orhorizontally in a gravitational frame of reference.

Furthermore, to the extent that the term “include,” “have,” or the likeis used in the description or the claims, such term is intended to beinclusive in a manner similar to the term “comprise” as “comprise” isinterpreted when employed as a transitional word in a claim.

The word “exemplary” is used herein to mean “serving as an example,instance, or illustration.” Any embodiment described herein as“exemplary” is not necessarily to be construed as preferred oradvantageous over other embodiments.

A reference to an element in the singular is not intended to mean “oneand only one” unless specifically stated, but rather “one or more.”Pronouns in the masculine (e.g., his) include the feminine and neutergender (e.g., her and its) and vice versa. The term “some” refers to oneor more. Underlined and/or italicized headings and subheadings are usedfor convenience only, do not limit the subject technology, and are notreferred to in connection with the interpretation of the description ofthe subject technology. All structural and functional equivalents to theelements of the various configurations described throughout thisdisclosure that are known or later come to be known to those of ordinaryskill in the art are expressly incorporated herein by reference andintended to be encompassed by the subject technology. Moreover, nothingdisclosed herein is intended to be dedicated to the public regardless ofwhether such disclosure is explicitly recited in the above description.

While certain aspects and embodiments of the subject technology havebeen described, these have been presented by way of example only, andare not intended to limit the scope of the subject technology. Indeed,the novel methods and systems described herein may be embodied in avariety of other forms without departing from the spirit thereof. Theaccompanying claims and their equivalents are intended to cover suchforms or modifications as would fall within the scope and spirit of thesubject technology.

What is claimed is:
 1. A slide comprising: a substrate forming aplurality of wells that are recessed relative to a surface of thesubstrate, wherein each of the wells forms a sample region that isrecessed by a sample depth from the surface and a trough region that isrecessed by a trough depth from the surface, the trough depth beinggreater than the sample depth.
 2. The slide of claim 1, wherein thesubstrate transmits electromagnetic radiation.
 3. The slide of claim 1,wherein the substrate is a salt.
 4. The slide of claim 1, wherein thesubstrate comprises AgBr, AgCl, Al₂O₃, AMTIR, BaF₂, CaF₂, CdTe, CsI,diamond, Ge, KBr, KCl, KRS-5, LiF, MgF₂, NaCl, Si, SiO₂, ZnS, ZnSe,and/or ZrO₂.
 5. The slide of claim 1, wherein a periphery of the slideforms a bilaterally asymmetric shape.
 6. The slide of claim 1, whereinthe trough region extends entirely about the sample region.
 7. The slideof claim 1, wherein the sample region is concentrically within thetrough region. 8-9. (canceled)
 10. A system comprising a slidecomprising: a substrate forming a plurality of wells that are recessedrelative to a surface of the substrate; a holder, comprising: a bodydefining a cavity between a first side and a second side of the body; aport for receiving the slide into the cavity; one or more firstfenestrations on the first side; and one or more second fenestrations onthe second side.
 11. The system of claim 10, further comprising a blockconfigured to secure the slide within the cavity when the block isplaced within the port.
 12. The system of claim 10, further comprising acover configured to enclose each of the wells when placed upon thesurface of the slide.
 13. The system of claim 12, wherein the cover isconfigured to transmit electromagnetic radiation.
 14. The system ofclaim 12, wherein the cover and the slide have a substantially equalthickness in a direction orthogonal to the surface of the slide when thecover is placed upon the surface of the slide.
 15. The system of claim10, wherein the body of the holder absorbs substantially allelectromagnetic radiation incident to the holder.
 16. The system ofclaim 10, wherein: the plurality of wells are provided in a plurality ofrows, each row comprises at least two of the plurality of wells, the oneor more first fenestrations comprises a number of first windows equal toa number of the plurality of rows, and the one or more secondfenestrations comprises a number of second windows equal to the numberof the plurality of rows. 17-26. (canceled)
 27. A method comprising:providing samples to each of a plurality of wells formed in a slide,each of the wells being recessed relative to a surface of the slide;enclosing the wells by applying a cover to the surface of the slide;inserting the slide and the cover into a cavity of a holder; andemitting electromagnetic radiation through one or more firstfenestrations of the holder, one or more second fenestrations of theholder, and the sample.
 28. The method of claim 27, further comprisinginserting the holder into a receptacle of a plate attached to an imagingdevice.
 29. (canceled)
 30. The method of claim 27, further comprisingheating the samples to a target temperature by conducting heat throughthe holder.
 31. The method of claim 27, further comprising placing a capin thermal contact with an outer surface of the holder. 32-35.(canceled)
 36. The method of claim 27, further comprising, after theemitting the electromagnetic radiation, detecting a characteristic ofthe electromagnetic radiation not absorbed by the sample.
 37. The methodof claim 27, further comprising: after the emitting the electromagneticradiation, changing the temperature of the sample; and emittingadditional electromagnetic radiation through the one or more firstfenestrations and the one or more second fenestrations of the holder andthrough the sample.